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In Print: Last Week's Sequencing-Related Papers of Note: Jun 19, 2012


Cooperativity in RNA-protein interactions: global analysis of RNA binding specificity.
Campbell ZT, Bhimsaria D, Valley CT, Rodriguez-Martinez JA, et al.
Cell Rep. 2012 May 31;1(5):570-581.

Analysis of insertion-deletion from deep-sequencing data: software evaluation for optimal detection.
Neuman JA, Isakov O, Shomron N.
Brief Bioinform. 2012 Mar 24. [Epub ahead of print]

Hybridization-based reconstruction of small non-coding RNA transcripts from deep sequencing data.
Ragan C, Mowry BJ, Bauer DC.
Nucleic Acids Res. 2012 Jun 16. [Epub ahead of print]

A pipeline for the identification and characterization of chromatin modifications derived from ChIP-seq datasets.
Kaspi A, Ziemann M, Rafehi H, Lazarus R, El-Osta A.
Biochimie. 2012 Jun 12. [Epub ahead of print]

Targeted re-sequencing of the allohexaploid wheat exome.
Winfield MO, Wilkinson PA, Allen AM, Barker GL, et al.
Plant Biotechnol J. 2012 Jun 18. [Epub ahead of print]

Characterisation of QTL-linked and genome-wide restriction site-associated DNA (RAD) markers in farmed Atlantic salmon.
Houston RD, Davey JW, Bishop SC, Lowe NR, et al.
BMC Genomics. 2012 Jun 15;13(1):244.

RNA polymerase II pausing downstream of core histone genes is different from genes producing polyadenylated transcripts.
Anamika K, Gyenis A, Poidevin L, Poch O, Tora L.
PLoS One. 2012;7(6):e38769.

A framework for human microbiome research.
Human Microbiome Project Consortium. Collaborators: Methé BA, Nelson KE, Pop M, Creasy HH, Giglio MG, Huttenhower C, Gevers D, Petrosino JF, et al.
Nature. 2012 Jun 13;486(7402):215-21.

Structure, function and diversity of the healthy human microbiome.
Human Microbiome Project Consortium. Collaborators: Huttenhower C, Gevers D, Knight R, et al.
Nature. 2012 Jun 13;486(7402):207-14.

Adsorption-driven translocation of polymer chain into nanopores.
Yang S, Neimark AV.
J Chem Phys. 2012 Jun 7;136(21):214901.

Normal and compound Poisson approximations for pattern occurrences in NGS reads.
Zhai Z, Reinert G, Song K, Waterman MS, et al.
J Comput Biol. 2012 Jun;19(6):839-54.

HapCompass: A fast cycle basis algorithm for accurate haplotype assembly of sequence data.
Aguiar D, Istrail S.
J Comput Biol. 2012 Jun;19(6):577-90.

A comparative transcriptomic analysis reveals conserved features of stem cell pluripotency in planarians and mammals.
Labbé RM, Irimia M, Currie KW, Lin A, et al.
Stem Cells. 2012 Jun 13. [Epub ahead of print]

VARIANT: Command line, web service and web interface for fast and accurate functional characterization of variants found by next-generation sequencing.
Medina I, De Maria A, Bleda M, Salavert F, et al.
Nucleic Acids Res. 2012 Jun 11. [Epub ahead of print]

Transcriptome analysis of microRNAs in developing cerebral cortex of rat.
Yao MJ, Chen G, Zhao PP, Lu MH, et al.
BMC Genomics. 2012 Jun 12;13(1):232.

Unzipping kinetics of duplex DNA containing oxidized lesions in an α-hemolysin nanopore.
Jin Q, Fleming AM, Burrows CJ, White HS.
J Am Chem Soc. 2012 Jun 12. [Epub ahead of print]

Repeat associated small RNAs vary among parents and following hybridization in maize.
Barber WT, Zhang W, Win H, Varala KK, et al.
Proc Natl Acad Sci U S A. 2012 Jun 11. [Epub ahead of print]

GenomeRing: alignment visualization based on SuperGenome coordinates.
Herbig A, Jäger G, Battke F, Nieselt K.
Bioinformatics. 2012 Jun 15;28(12):i7-i15.

NORMAL: accurate nucleosome positioning using a modified Gaussian mixture model.
Polishko A, Ponts N, Le Roch KG, Lonardi S.
Bioinformatics. 2012 Jun 15;28(12):i242-i249.

Weighted pooling — practical and cost-effective techniques for pooled high-throughput sequencing.
Golan D, Erlich Y, Rosset S.
Bioinformatics. 2012 Jun 15;28(12):i197-i206.

SEQuel: improving the accuracy of genome assemblies.
Ronen R, Boucher C, Chitsaz H, Pevzner P.
Bioinformatics. 2012 Jun 15;28(12):i188-i196.

Xenome — a tool for classifying reads from xenograft samples.
Conway T, Wazny J, Bromage A, Tymms M, et al.
Bioinformatics. 2012 Jun 15;28(12):i172-i178.

BatMis: A fast algorithm for k-mismatch mapping.
Tennakoon C, Purbojati RW, Sung WK.
Bioinformatics. 2012 Jun 10. [Epub ahead of print]

SAAP-RRBS: Streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing.
Sun Z, Baheti S, Middha S, Kanwar R, et al.
Bioinformatics. 2012 Jun 10. [Epub ahead of print]

Length distribution of sequencing by synthesis: fixed flow cycle model.
Kong Y.
Math Biol. 2012 Jun 12. [Epub ahead of print]

Metagenomic microbial community profiling using unique clade-specific marker genes.
Segata N, Waldron L, Ballarini A, Narasimhan V, et al.
Nat Methods. 2012 Jun 10. [Epub ahead of print]

MicroRNA expression profiling of hypothalamic arcuate and paraventricular nuclei from single rats using Illumina sequencing technology.
Amar L, Benoit C, Beaumont G, Vacher CM, et al.
J Neurosci Methods. 2012 Jun 8. [Epub ahead of print]

Integrative analyses for omics data: A Bayesian mixture model to assess the concordance of ChIP-chip and ChIP-seq measurements.
Schäfer M, Lkhagvasuren O, Klein HU, Elling C, et al.
Toxicol Environ Health A. 2012 Apr 15;75(8-10):461-70.

PANDAseq: paired-end assembler for Illumina sequences.
Masella AP, Bartram AK, Truszkowski JM, Brown DG, Neufeld JD.
BMC Bioinformatics. 2012 Feb 14;13:31.

The Scan

NFTs for Genome Sharing

Nature News writes that non-fungible tokens could be a way for people to profit from sharing genomic data.

Wastewater Warning System

Time magazine writes that cities and college campuses are monitoring sewage for SARS-CoV-2, an approach officials hope lasts beyond COVID-19.

Networks to Boost Surveillance

Scientific American writes that new organizations and networks aim to improve the ability of developing countries to conduct SARS-CoV-2 genomic surveillance.

Genome Biology Papers on Gastric Cancer Epimutations, BUTTERFLY, GUNC Tool

In Genome Biology this week: recurrent epigenetic mutations in gastric cancer, correction tool for unique molecular identifier-based assays, and more.